Genome-wide CNV analysis replicates the association between GSTM1 deletion and bladder cancer: a support for using continuous measurement from SNP-array data

Marenne, Gaëlle; Real, Francisco X.; Rothman, Nathaniel; Rodríguez Santiago, Benjamín; Pérez Jurado, Luis Alberto; Kogevinas, Manolis; García Closas, Montserrat; Silverman, Debra T.; Chanock, Stephen J.; Génin, Emmanuelle; Malats i Riera, Núria

Genome-wide CNV analysis replicates the association between GSTM1 deletion and bladder cancer: a support for using continuous measurement from SNP-array data

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dc.contributor.author Marenne, Gaëlleca
dc.contributor.author Real, Francisco X.ca
dc.contributor.author Rothman, Nathanielca
dc.contributor.author Rodríguez Santiago, Benjamínca
dc.contributor.author Pérez Jurado, Luis Albertoca
dc.contributor.author Kogevinas, Manolisca
dc.contributor.author García Closas, Montserratca
dc.contributor.author Silverman, Debra T.ca
dc.contributor.author Chanock, Stephen J.ca
dc.contributor.author Génin, Emmanuelleca
dc.contributor.author Malats i Riera, Núriaca
dc.date.accessioned 2015-03-10T10:40:29Z
dc.date.available 2015-03-10T10:40:29Z
dc.date.issued 2012ca
dc.description.abstract BACKGROUND: Structural variations such as copy number variants (CNV) influence the expression of different phenotypic traits. Algorithms to identify CNVs through SNP-array platforms are available. The ability to evaluate well-characterized CNVs such as GSTM1 (1p13.3) deletion provides an important opportunity to assess their performance. RESULTS: 773 cases and 759 controls from the SBC/EPICURO Study were genotyped in the GSTM1 region using TaqMan, Multiplex Ligation-dependent Probe Amplification (MLPA), and Illumina Infinium 1 M SNP-array platforms. CNV callings provided by TaqMan and MLPA were highly concordant and replicated the association between GSTM1 and bladder cancer. This was not the case when CNVs were called using Illumina 1 M data through available algorithms since no deletion was detected across the study samples. In contrast, when the Log R Ratio (LRR) was used as a continuous measure for the 5 probes contained in this locus, we were able to detect their association with bladder cancer using simple regression models or more sophisticated methods such as the ones implemented in the CNVtools package. CONCLUSIONS: This study highlights an important limitation in the CNV calling from SNP-array data in regions of common aberrations and suggests that there may be added advantage for using LRR as a continuous measure in association tests rather than relying on calling algorithms.
dc.description.sponsorship This work was partially supported by the Fondo de Investigación Sanitaria, Spain (G03/174, PI051436, PI061614, FI09/00205); Acc.Integrada Hispano-Francesa, Ministerio de Ciencia e Innovación (HF2008-0069), Red Temática de Investigación Cooperativa en Cáncer (RTICC), Instituto de Salud Carlos III, Ministry of Health, Spain; the Intramural Research Program of the Division of Cancer Epidemiology and Genetics, National Cancer Institute, USA; and by the EU (HEALTH-F2-2008-201663); and by Egide-PHRC Picasso travel grant.
dc.format.mimetype application/pdfca
dc.identifier.citation Marenne G, Real FX, Rothman N, Rodríguez-Santiago B, Pérez-Jurado L, Kogevinas M et al. Genome-wide CNV analysis replicates the association between GSTM1 deletion and bladder cancer: a support for using continuous measurement from SNP-array data. BMC Genomics. 2012;13:326. DOI: 10.1186/1471-2164-13-326ca
dc.identifier.doi http://dx.doi.org/10.1186/1471-2164-13-326
dc.identifier.issn 1471-2164ca
dc.identifier.uri http://hdl.handle.net/10230/23176
dc.language.iso engca
dc.publisher BioMed Centralca
dc.relation.ispartof BMC Genomics. 2012;13:326
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/201663ca
dc.rights © 2012 Marenne et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.ca
dc.rights.accessRights info:eu-repo/semantics/openAccessca
dc.rights.uri http://creativecommons.org/licenses/by/2.0
dc.subject.keyword Bladder cancer risken
dc.subject.keyword Glutathione S-transferase mu 1 (GSTM1)en
dc.subject.keyword Copy number variation (CNV)en
dc.subject.keyword SNP-arrayen
dc.subject.other Bufeta -- Càncerca
dc.title Genome-wide CNV analysis replicates the association between GSTM1 deletion and bladder cancer: a support for using continuous measurement from SNP-array dataca
dc.type info:eu-repo/semantics/articleca
dc.type.version info:eu-repo/semantics/publishedVersionca

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